Efficacy of Microarray Profiling Data Combined with QTL Mapping for the Identification of a QTL Gene Controlling the Initial Growth Rate in Rice

Abstract

Seedling vigor, which is controlled by many quantitative trait loci (QTLs), is one of several important agronomic traits for direct-seedling rice systems. However, isolating these QTL genes is laborious and expensive. Here, we combined QTL mapping and microarray profiling to identify QTL genes for seedling vigor. By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, early-stage plant development1/2 (qEPD1 and qEPD2), whose Koshihikari alleles promote plant height and/or leaf sheath length. Phenotypic analysis of the two substituted lines carrying the Habataki qEPD1 or qEPD2 allele revealed that qEPD2 functioned more dominantly for the initial growth of rice. From the microarray experiment, 55 and 45 candidate genes were found in the qEPD1 and qEPD2 genomic regions, which are expressed differentially between each substitution line (SL) and Koshihikari. Gibberellin 20 oxidase-2 (OsGA20ox2), which is identical to Semi Dwarf1 (SD1), was included among the 55 candidate genes of qEPD1, whereas its paralog, OsGA20ox1, was included among the 45 candidate genes of qEPD2. Consistently, introduction of the Koshihikari OsGA20ox1 allele into SL(qEPD2) increaseed its plant height and leaf sheath length significantly relative to the introduction of the Habataki OsGA20ox1 allele. Therefore, microarray profiling could be useful for rapidly screening QTL candidate genes. We concluded that OsGA20ox1 and OsGA20ox2 (SD1) function during the initial growth of rice, but OsGA20ox1 plays a dominant role in increasing plant height and leaf sheath length at the initial growth stage.

QTLs for Shoot Length and Chlorophyll Content of Rice Seedlings Grown under Low-Temperature Conditions, using a Cross between Indica and Japonica Cultivars

“…Therefore, OsGA20ox2 is thought to be a key component of the QTLs for shoot and culm length in this study. The previous study suggested that OsGA20ox2 affected the shoot length at 25ºC conditions (Yano et al, 2012). In this study, qSL1 containing OsGA20ox2 affected the shoot length at 16ºC, suggesting that this region affects the shoot growth rate in the low-temperature conditions as well as in the warm conditions.…”

“…The most effective QTL in increasing the shoot length via the Arroz da Terra allele, qSL1, was detected in the Chr .1 2 3 4 5 6 7 8 9 10 11 12 RM5423 RM8105 RM3233 RM2770 RM4355 RM4108 RM1248 RM1200 RM5579 RM6517 RM6467 RM3408 RM5752 RM1353 RM7479 RM8010 RM6369 RM6356 RM8018 RM1148 RM3892 RM7492 RM3882 RM7217 RM286 RM1812 et al, 2000), D10 (Arite et al, 2007), THIS1 (Liu et al, 2013), Psd1 (Li et al, 2014), CIGR (Kovi et al, 2011), SD1 (Sasaki et al, 2002;Ashikari et al, 2005. Yano et al, 2012 and SPS (Ishimaru et al, 2004).…”

“…As a result, a different QTL linked to the low-temperature germinability gene was detected. Additionally, OsGA20ox1, an isoform of OsGA20ox2, known to affect the initial growth rate of the shoot (Abe et al, 2012;Yano et al, 2012), has been located on chromosome 3. However, it was localized in a position different from that of qSL3 detected in this study (Fig.…”

The need for new tools and investment to improve the accuracy of selecting for grain quality in rice

“…Advances in molecular techniques have made high-throughput genotyping (Collard et al, 2008;Thomson et al, 2012), genome sequencing (Huang et al, 2013), and transcriptomics (Yano et al, 2012) faster and more affordable. In conjunction with this, progress in bioinformatics tools and the availability of genomics databases have made the processing of molecular information easier and more accessible to the scientific community.…”

QTLs for Seedling Growth of Direct Seeded Rice under Submerged and Low Temperature Conditions

“…Quantitative trait loci (QTL) analysis and identification of genes affecting seedling vigor are necessary to identify genetic markers. QTLs affecting seedling vigor, low temperature germinability (Suh et al, 1999;Miura et al, 2001;Fujino et al, 2004;Zhang et al, 2005aZhang et al, , 2005bJiang et al, 2006;Ji et al, 2009), coleoptile elongation rate under various iron concentrations (Ouyang et al, 2007), shoot length (Zhang et al, 2005a(Zhang et al, , 2005bZhou et al, 2007;Abe et al, 2012;Yano et al, 2012), and seedling emergence under field conditions (Zhou et al, 2007;Iwata et al, 2010) have been reported. These studies suggested that seedling vigor is affected by many genetic and environmental factors.…”